Starting phenix.real_space_refine on Fri Mar 6 22:42:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ttt_26123/03_2026/7ttt_26123.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ttt_26123/03_2026/7ttt_26123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ttt_26123/03_2026/7ttt_26123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ttt_26123/03_2026/7ttt_26123.map" model { file = "/net/cci-nas-00/data/ceres_data/7ttt_26123/03_2026/7ttt_26123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ttt_26123/03_2026/7ttt_26123.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 8 5.89 5 P 16 5.49 5 Mg 8 5.21 5 S 213 5.16 5 C 21988 2.51 5 N 6103 2.21 5 O 6820 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35180 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2750 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain breaks: 1 Chain: "B" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "C" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4003 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 15, 'TRANS': 505} Chain breaks: 1 Chain: "D" Number of atoms: 4072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4072 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 18, 'TRANS': 509} Chain: "E" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3960 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 11, 'TRANS': 514} Chain: "F" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3924 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "G" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4063 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 14, 'TRANS': 520} Chain: "H" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4064 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "I" Number of atoms: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4051 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 14, 'TRANS': 513} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.66, per 1000 atoms: 0.22 Number of scatterers: 35180 At special positions: 0 Unit cell: (181.5, 184.8, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 213 16.00 P 16 15.00 Al 8 13.00 Mg 8 11.99 F 24 9.00 O 6820 8.00 N 6103 7.00 C 21988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8488 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 52 sheets defined 55.2% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.683A pdb=" N LYS A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.681A pdb=" N ASP A 45 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 3.720A pdb=" N ASP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.677A pdb=" N LYS A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 180 through 194 removed outlier: 3.573A pdb=" N HIS A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU A 194 " --> pdb=" O HIS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.165A pdb=" N ILE A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A 212 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 242 removed outlier: 4.767A pdb=" N LEU A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N CYS A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 258 removed outlier: 4.162A pdb=" N ASN A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.742A pdb=" N LEU A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 404 through 424 removed outlier: 4.418A pdb=" N PHE A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.627A pdb=" N THR B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 80 through 97 Processing helix chain 'B' and resid 100 through 122 removed outlier: 4.025A pdb=" N VAL B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 143 Processing helix chain 'B' and resid 144 through 147 removed outlier: 3.568A pdb=" N VAL B 147 " --> pdb=" O PRO B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'B' and resid 156 through 164 removed outlier: 3.677A pdb=" N SER B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.577A pdb=" N ILE B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.534A pdb=" N LEU B 179 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.690A pdb=" N LEU B 265 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 381 through 405 Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 434 through 445 removed outlier: 3.604A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 474 removed outlier: 3.545A pdb=" N VAL B 463 " --> pdb=" O LYS B 459 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 501 through 520 Processing helix chain 'C' and resid 18 through 36 removed outlier: 3.649A pdb=" N LEU C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 40 removed outlier: 4.092A pdb=" N LEU C 40 " --> pdb=" O ARG C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 37 through 40' Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 76 through 90 removed outlier: 3.742A pdb=" N VAL C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 114 removed outlier: 3.618A pdb=" N VAL C 108 " --> pdb=" O PHE C 104 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 117 through 140 removed outlier: 3.891A pdb=" N ILE C 121 " --> pdb=" O HIS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 163 Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 171 through 184 removed outlier: 4.048A pdb=" N LYS C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET C 178 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 204 through 208 removed outlier: 3.715A pdb=" N SER C 208 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.975A pdb=" N GLN C 228 " --> pdb=" O PHE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 283 removed outlier: 3.827A pdb=" N GLU C 270 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TRP C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 removed outlier: 3.618A pdb=" N ARG C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 338 through 342 removed outlier: 3.563A pdb=" N VAL C 341 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 342 " --> pdb=" O ALA C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 342' Processing helix chain 'C' and resid 378 through 402 removed outlier: 3.685A pdb=" N ASP C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 392 " --> pdb=" O SER C 388 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS C 401 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 425 removed outlier: 3.566A pdb=" N ARG C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 441 removed outlier: 3.892A pdb=" N LEU C 433 " --> pdb=" O GLY C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 454 removed outlier: 3.892A pdb=" N ARG C 447 " --> pdb=" O GLU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.582A pdb=" N ILE C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 525 Processing helix chain 'D' and resid 30 through 49 Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.626A pdb=" N GLU D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 149 removed outlier: 3.726A pdb=" N ASP D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'D' and resid 175 through 180 removed outlier: 6.595A pdb=" N VAL D 178 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER D 180 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 197 Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 270 through 295 removed outlier: 3.698A pdb=" N TYR D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 317 Processing helix chain 'D' and resid 326 through 338 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.920A pdb=" N LEU D 353 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 415 Processing helix chain 'D' and resid 423 through 438 Processing helix chain 'D' and resid 444 through 455 Processing helix chain 'D' and resid 456 through 467 removed outlier: 3.949A pdb=" N MET D 460 " --> pdb=" O GLU D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 484 Processing helix chain 'D' and resid 510 through 529 Processing helix chain 'E' and resid 20 through 40 removed outlier: 3.652A pdb=" N VAL E 39 " --> pdb=" O ILE E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 66 through 74 removed outlier: 3.688A pdb=" N ASN E 73 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 95 removed outlier: 3.520A pdb=" N LYS E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 119 removed outlier: 3.552A pdb=" N VAL E 102 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR E 103 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 144 Processing helix chain 'E' and resid 151 through 167 Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 175 through 189 removed outlier: 3.629A pdb=" N GLU E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.705A pdb=" N SER E 212 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 284 removed outlier: 3.733A pdb=" N VAL E 264 " --> pdb=" O SER E 260 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 307 removed outlier: 3.522A pdb=" N ALA E 307 " --> pdb=" O LEU E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 328 Processing helix chain 'E' and resid 337 through 341 removed outlier: 3.783A pdb=" N VAL E 341 " --> pdb=" O PRO E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 403 removed outlier: 3.750A pdb=" N ASP E 392 " --> pdb=" O ARG E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 426 Processing helix chain 'E' and resid 430 through 444 removed outlier: 4.378A pdb=" N VAL E 434 " --> pdb=" O GLY E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 454 removed outlier: 3.971A pdb=" N THR E 448 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E 454 " --> pdb=" O ILE E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.613A pdb=" N ARG E 516 " --> pdb=" O GLU E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 49 Processing helix chain 'F' and resid 50 through 52 No H-bonds generated for 'chain 'F' and resid 50 through 52' Processing helix chain 'F' and resid 73 through 81 Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.645A pdb=" N LEU F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 127 removed outlier: 4.042A pdb=" N VAL F 110 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 152 removed outlier: 3.638A pdb=" N GLU F 146 " --> pdb=" O GLU F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 172 removed outlier: 3.845A pdb=" N LEU F 163 " --> pdb=" O ASP F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 193 Proline residue: F 185 - end of helix removed outlier: 3.583A pdb=" N VAL F 188 " --> pdb=" O SER F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 206 No H-bonds generated for 'chain 'F' and resid 204 through 206' Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 268 through 293 removed outlier: 4.142A pdb=" N MET F 272 " --> pdb=" O ASP F 268 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU F 276 " --> pdb=" O MET F 272 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR F 293 " --> pdb=" O GLN F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'F' and resid 332 through 341 Processing helix chain 'F' and resid 347 through 351 Processing helix chain 'F' and resid 352 through 356 removed outlier: 3.847A pdb=" N LEU F 356 " --> pdb=" O ALA F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 418 Processing helix chain 'F' and resid 426 through 443 removed outlier: 3.762A pdb=" N ARG F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR F 442 " --> pdb=" O GLU F 438 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 443 " --> pdb=" O TYR F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 457 removed outlier: 3.947A pdb=" N TYR F 449 " --> pdb=" O GLY F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 469 removed outlier: 3.737A pdb=" N ALA F 469 " --> pdb=" O LEU F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 504 through 507 Processing helix chain 'F' and resid 512 through 530 Processing helix chain 'G' and resid 14 through 33 removed outlier: 3.532A pdb=" N ARG G 18 " --> pdb=" O GLY G 14 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 65 Processing helix chain 'G' and resid 69 through 86 removed outlier: 4.217A pdb=" N LEU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 110 removed outlier: 3.866A pdb=" N GLN G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 133 removed outlier: 3.514A pdb=" N VAL G 117 " --> pdb=" O HIS G 113 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN G 133 " --> pdb=" O VAL G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 157 Processing helix chain 'G' and resid 164 through 178 Processing helix chain 'G' and resid 204 through 208 Processing helix chain 'G' and resid 256 through 258 No H-bonds generated for 'chain 'G' and resid 256 through 258' Processing helix chain 'G' and resid 259 through 280 removed outlier: 3.827A pdb=" N ILE G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR G 271 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS G 272 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS G 277 " --> pdb=" O GLU G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 304 removed outlier: 3.788A pdb=" N LYS G 298 " --> pdb=" O ASP G 294 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR G 299 " --> pdb=" O MET G 295 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE G 300 " --> pdb=" O CYS G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 324 Processing helix chain 'G' and resid 341 through 345 removed outlier: 3.838A pdb=" N MET G 344 " --> pdb=" O GLU G 341 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU G 345 " --> pdb=" O ALA G 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 341 through 345' Processing helix chain 'G' and resid 381 through 405 removed outlier: 3.710A pdb=" N ASP G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 427 Processing helix chain 'G' and resid 428 through 430 No H-bonds generated for 'chain 'G' and resid 428 through 430' Processing helix chain 'G' and resid 433 through 445 removed outlier: 3.993A pdb=" N ALA G 437 " --> pdb=" O ARG G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 456 removed outlier: 3.789A pdb=" N ASN G 450 " --> pdb=" O LEU G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 476 Processing helix chain 'G' and resid 477 through 484 removed outlier: 5.317A pdb=" N ASN G 482 " --> pdb=" O GLU G 479 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS G 484 " --> pdb=" O LYS G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 502 Processing helix chain 'G' and resid 507 through 526 removed outlier: 3.747A pdb=" N ARG G 526 " --> pdb=" O ILE G 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 38 removed outlier: 3.855A pdb=" N GLN H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE H 36 " --> pdb=" O THR H 32 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 74 through 91 Processing helix chain 'H' and resid 96 through 108 Processing helix chain 'H' and resid 109 through 114 Processing helix chain 'H' and resid 118 through 140 removed outlier: 3.787A pdb=" N VAL H 122 " --> pdb=" O HIS H 118 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP H 132 " --> pdb=" O LYS H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 161 Processing helix chain 'H' and resid 163 through 167 removed outlier: 3.645A pdb=" N SER H 166 " --> pdb=" O LYS H 163 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG H 167 " --> pdb=" O ALA H 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 163 through 167' Processing helix chain 'H' and resid 168 through 184 removed outlier: 3.806A pdb=" N ASN H 174 " --> pdb=" O SER H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 212 Processing helix chain 'H' and resid 262 through 284 removed outlier: 3.540A pdb=" N GLU H 271 " --> pdb=" O ILE H 267 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 307 Processing helix chain 'H' and resid 316 through 328 Processing helix chain 'H' and resid 334 through 338 Processing helix chain 'H' and resid 380 through 404 Processing helix chain 'H' and resid 412 through 427 removed outlier: 3.868A pdb=" N LYS H 427 " --> pdb=" O THR H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 443 removed outlier: 3.945A pdb=" N ALA H 441 " --> pdb=" O TYR H 437 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 456 Processing helix chain 'H' and resid 458 through 471 removed outlier: 3.886A pdb=" N THR H 464 " --> pdb=" O ILE H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 494 Processing helix chain 'H' and resid 499 through 517 Processing helix chain 'I' and resid 15 through 35 removed outlier: 3.805A pdb=" N LEU I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA I 21 " --> pdb=" O GLN I 17 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 67 Processing helix chain 'I' and resid 71 through 88 removed outlier: 3.567A pdb=" N ILE I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 111 removed outlier: 3.625A pdb=" N ASN I 95 " --> pdb=" O GLY I 91 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL I 96 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR I 109 " --> pdb=" O GLN I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 138 removed outlier: 4.160A pdb=" N ILE I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU I 136 " --> pdb=" O GLN I 132 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS I 138 " --> pdb=" O LEU I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 157 Processing helix chain 'I' and resid 161 through 179 removed outlier: 3.636A pdb=" N VAL I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 204 Processing helix chain 'I' and resid 252 through 263 Processing helix chain 'I' and resid 264 through 282 removed outlier: 4.191A pdb=" N ARG I 270 " --> pdb=" O PHE I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 307 Processing helix chain 'I' and resid 319 through 328 removed outlier: 4.048A pdb=" N THR I 325 " --> pdb=" O MET I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 404 removed outlier: 3.941A pdb=" N LEU I 384 " --> pdb=" O ASN I 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 424 removed outlier: 3.673A pdb=" N LYS I 424 " --> pdb=" O GLU I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 445 removed outlier: 4.034A pdb=" N GLY I 436 " --> pdb=" O ARG I 432 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU I 445 " --> pdb=" O ALA I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 455 removed outlier: 3.504A pdb=" N LYS I 449 " --> pdb=" O LEU I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 458 through 469 removed outlier: 3.527A pdb=" N GLU I 469 " --> pdb=" O LYS I 465 " (cutoff:3.500A) Processing helix chain 'I' and resid 489 through 493 Processing helix chain 'I' and resid 497 through 517 removed outlier: 3.753A pdb=" N LYS I 501 " --> pdb=" O ASN I 497 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU I 517 " --> pdb=" O THR I 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 removed outlier: 8.682A pdb=" N VAL A 91 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 65 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ILE A 64 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N HIS A 6 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL A 66 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN A 8 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLU A 3 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A 132 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 5 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER A 138 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLN A 131 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ASN A 165 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 133 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N PHE A 167 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU A 135 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL A 169 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N HIS A 137 " --> pdb=" O VAL A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 removed outlier: 8.682A pdb=" N VAL A 91 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 65 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ILE A 64 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N HIS A 6 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL A 66 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN A 8 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLU A 3 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A 132 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 5 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER A 138 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLN A 131 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ASN A 165 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 133 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N PHE A 167 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU A 135 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL A 169 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N HIS A 137 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET A 164 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N TYR A 200 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR A 166 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR A 199 " --> pdb=" O PHE A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 22 removed outlier: 6.684A pdb=" N MET I 44 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN B 523 " --> pdb=" O MET I 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 63 through 66 removed outlier: 7.835A pdb=" N ASN B 53 " --> pdb=" O ASP C 527 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR C 529 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET B 55 " --> pdb=" O THR C 529 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LYS C 531 " --> pdb=" O MET B 55 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 57 " --> pdb=" O LYS C 531 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 208 removed outlier: 3.823A pdb=" N GLY B 379 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.665A pdb=" N VAL B 350 " --> pdb=" O VAL B 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AA9, first strand: chain 'B' and resid 255 through 259 removed outlier: 3.539A pdb=" N ARG C 256 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N LYS D 265 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 255 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP D 267 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C 257 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N GLN F 263 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL E 256 " --> pdb=" O GLN F 263 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL F 265 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 258 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLN G 251 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE F 264 " --> pdb=" O GLN G 251 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL G 253 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL F 266 " --> pdb=" O VAL G 253 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ASP H 255 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL G 252 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLU H 257 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE G 254 " --> pdb=" O GLU H 257 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN I 245 " --> pdb=" O THR H 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 408 through 410 Processing sheet with id=AB2, first strand: chain 'B' and resid 478 through 480 Processing sheet with id=AB3, first strand: chain 'C' and resid 56 through 59 removed outlier: 6.369A pdb=" N ASP C 46 " --> pdb=" O ILE D 530 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP D 532 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 535 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 195 through 201 removed outlier: 6.505A pdb=" N GLY C 196 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU C 374 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS C 198 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY C 376 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL C 200 " --> pdb=" O GLY C 376 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 213 through 217 Processing sheet with id=AB6, first strand: chain 'C' and resid 309 through 311 Processing sheet with id=AB7, first strand: chain 'C' and resid 405 through 407 Processing sheet with id=AB8, first strand: chain 'C' and resid 485 through 488 Processing sheet with id=AB9, first strand: chain 'D' and resid 68 through 71 removed outlier: 7.213A pdb=" N ASP D 58 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ILE E 521 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET D 60 " --> pdb=" O ILE E 521 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC2, first strand: chain 'D' and resid 209 through 213 removed outlier: 6.763A pdb=" N LYS D 210 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 387 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLU D 212 " --> pdb=" O ILE D 387 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 228 through 230 Processing sheet with id=AC4, first strand: chain 'D' and resid 321 through 322 removed outlier: 8.988A pdb=" N VAL D 342 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 250 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 321 through 322 Processing sheet with id=AC6, first strand: chain 'E' and resid 61 through 64 removed outlier: 7.271A pdb=" N ASP E 49 " --> pdb=" O ASP F 534 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL F 536 " --> pdb=" O ASP E 49 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE E 51 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR F 538 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU E 53 " --> pdb=" O THR F 538 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=AC8, first strand: chain 'E' and resid 199 through 205 removed outlier: 4.206A pdb=" N GLY E 377 " --> pdb=" O LYS E 204 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 218 through 220 removed outlier: 3.641A pdb=" N CYS E 346 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU E 348 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLU E 233 " --> pdb=" O LEU E 348 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE E 290 " --> pdb=" O ILE E 312 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 218 through 220 removed outlier: 3.641A pdb=" N CYS E 346 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU E 348 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLU E 233 " --> pdb=" O LEU E 348 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ALA E 332 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE E 239 " --> pdb=" O ALA E 332 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AD3, first strand: chain 'F' and resid 68 through 71 removed outlier: 6.299A pdb=" N ASP F 58 " --> pdb=" O ILE G 527 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP G 529 " --> pdb=" O ASP F 58 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AD5, first strand: chain 'F' and resid 208 through 214 removed outlier: 6.513A pdb=" N LYS F 209 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL F 390 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 211 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLY F 392 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS F 213 " --> pdb=" O GLY F 392 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 226 through 229 removed outlier: 4.041A pdb=" N GLY F 371 " --> pdb=" O LEU F 367 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N CYS F 379 " --> pdb=" O ALA F 359 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA F 359 " --> pdb=" O CYS F 379 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU F 361 " --> pdb=" O GLU F 242 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU F 242 " --> pdb=" O LEU F 361 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU F 363 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG F 240 " --> pdb=" O GLU F 363 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 491 through 494 Processing sheet with id=AD8, first strand: chain 'G' and resid 52 through 55 removed outlier: 5.857A pdb=" N ASP G 42 " --> pdb=" O ILE H 519 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP H 521 " --> pdb=" O ASP G 42 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 196 through 199 removed outlier: 6.432A pdb=" N ASN G 196 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU G 377 " --> pdb=" O ASN G 196 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU G 198 " --> pdb=" O LEU G 377 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 213 through 216 removed outlier: 6.839A pdb=" N THR G 367 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA G 348 " --> pdb=" O THR G 367 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 213 through 216 removed outlier: 6.839A pdb=" N THR G 367 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA G 348 " --> pdb=" O THR G 367 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 408 through 410 Processing sheet with id=AE4, first strand: chain 'H' and resid 57 through 60 removed outlier: 7.785A pdb=" N MET H 47 " --> pdb=" O ASP I 519 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE I 521 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET H 49 " --> pdb=" O ILE I 521 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG I 523 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU H 51 " --> pdb=" O ARG I 523 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 142 through 143 Processing sheet with id=AE6, first strand: chain 'H' and resid 185 through 186 Processing sheet with id=AE7, first strand: chain 'H' and resid 199 through 205 removed outlier: 4.089A pdb=" N GLY H 378 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR H 373 " --> pdb=" O LEU H 215 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 218 through 220 Processing sheet with id=AE9, first strand: chain 'H' and resid 310 through 312 removed outlier: 9.161A pdb=" N VAL H 332 " --> pdb=" O ILE H 238 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU H 240 " --> pdb=" O VAL H 332 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 478 through 480 Processing sheet with id=AF2, first strand: chain 'I' and resid 139 through 140 Processing sheet with id=AF3, first strand: chain 'I' and resid 191 through 196 removed outlier: 6.435A pdb=" N GLU I 192 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE I 376 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET I 194 " --> pdb=" O ILE I 376 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 210 through 212 Processing sheet with id=AF5, first strand: chain 'I' and resid 311 through 313 removed outlier: 6.237A pdb=" N TYR I 229 " --> pdb=" O VAL I 290 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE I 292 " --> pdb=" O TYR I 229 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU I 231 " --> pdb=" O ILE I 292 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N LEU I 333 " --> pdb=" O ILE I 230 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR I 232 " --> pdb=" O LEU I 333 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 311 through 313 removed outlier: 6.237A pdb=" N TYR I 229 " --> pdb=" O VAL I 290 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE I 292 " --> pdb=" O TYR I 229 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU I 231 " --> pdb=" O ILE I 292 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 477 through 479 2029 hydrogen bonds defined for protein. 5787 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.83 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6136 1.28 - 1.42: 7656 1.42 - 1.55: 21406 1.55 - 1.68: 37 1.68 - 1.82: 370 Bond restraints: 35605 Sorted by residual: bond pdb=" F1 AF3 B 603 " pdb="AL AF3 B 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" F3 AF3 I 603 " pdb="AL AF3 I 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F3 AF3 H 603 " pdb="AL AF3 H 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F3 AF3 E 603 " pdb="AL AF3 E 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F1 AF3 E 603 " pdb="AL AF3 E 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.68e+01 ... (remaining 35600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 46941 1.92 - 3.84: 900 3.84 - 5.75: 188 5.75 - 7.67: 55 7.67 - 9.59: 10 Bond angle restraints: 48094 Sorted by residual: angle pdb=" CA ASP G 528 " pdb=" CB ASP G 528 " pdb=" CG ASP G 528 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.00e+00 1.00e+00 4.36e+01 angle pdb=" CA PHE B 191 " pdb=" CB PHE B 191 " pdb=" CG PHE B 191 " ideal model delta sigma weight residual 113.80 120.00 -6.20 1.00e+00 1.00e+00 3.84e+01 angle pdb=" C GLY C 41 " pdb=" N PRO C 42 " pdb=" CA PRO C 42 " ideal model delta sigma weight residual 119.56 125.71 -6.15 1.01e+00 9.80e-01 3.71e+01 angle pdb=" CA ASP B 230 " pdb=" CB ASP B 230 " pdb=" CG ASP B 230 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.00e+00 1.00e+00 3.45e+01 angle pdb=" CA ALA A 271 " pdb=" C ALA A 271 " pdb=" N PRO A 272 " ideal model delta sigma weight residual 118.44 127.49 -9.05 1.59e+00 3.96e-01 3.24e+01 ... (remaining 48089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 21339 35.50 - 71.00: 556 71.00 - 106.49: 45 106.49 - 141.99: 6 141.99 - 177.49: 6 Dihedral angle restraints: 21952 sinusoidal: 8835 harmonic: 13117 Sorted by residual: dihedral pdb=" C5' ADP E 602 " pdb=" O5' ADP E 602 " pdb=" PA ADP E 602 " pdb=" O2A ADP E 602 " ideal model delta sinusoidal sigma weight residual -60.00 117.49 -177.49 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP C 602 " pdb=" O3A ADP C 602 " pdb=" PA ADP C 602 " pdb=" PB ADP C 602 " ideal model delta sinusoidal sigma weight residual -60.00 113.95 -173.94 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP B 602 " pdb=" O3A ADP B 602 " pdb=" PA ADP B 602 " pdb=" PB ADP B 602 " ideal model delta sinusoidal sigma weight residual 300.00 127.11 172.89 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 21949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4999 0.067 - 0.133: 650 0.133 - 0.200: 39 0.200 - 0.267: 5 0.267 - 0.333: 5 Chirality restraints: 5698 Sorted by residual: chirality pdb=" CB VAL C 406 " pdb=" CA VAL C 406 " pdb=" CG1 VAL C 406 " pdb=" CG2 VAL C 406 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ALA A 271 " pdb=" N ALA A 271 " pdb=" C ALA A 271 " pdb=" CB ALA A 271 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA LYS C 401 " pdb=" N LYS C 401 " pdb=" C LYS C 401 " pdb=" CB LYS C 401 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 5695 not shown) Planarity restraints: 6157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 269 " 0.027 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C GLY A 269 " -0.095 2.00e-02 2.50e+03 pdb=" O GLY A 269 " 0.036 2.00e-02 2.50e+03 pdb=" N PHE A 270 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 189 " 0.025 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C SER B 189 " -0.085 2.00e-02 2.50e+03 pdb=" O SER B 189 " 0.031 2.00e-02 2.50e+03 pdb=" N ILE B 190 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 197 " -0.016 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C PHE B 197 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE B 197 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 198 " -0.020 2.00e-02 2.50e+03 ... (remaining 6154 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 138 2.50 - 3.10: 24576 3.10 - 3.70: 49289 3.70 - 4.30: 71533 4.30 - 4.90: 125777 Nonbonded interactions: 271313 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O1A ADP B 602 " model vdw 1.898 2.170 nonbonded pdb="MG MG G 601 " pdb=" F1 AF3 G 603 " model vdw 1.906 2.120 nonbonded pdb="MG MG B 601 " pdb=" O1B ADP B 602 " model vdw 1.938 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1A ADP C 602 " model vdw 1.958 2.170 nonbonded pdb="MG MG H 601 " pdb=" O1B ADP H 602 " model vdw 1.978 2.170 ... (remaining 271308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.270 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.280 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.533 35606 Z= 0.411 Angle : 0.706 9.589 48094 Z= 0.401 Chirality : 0.046 0.333 5698 Planarity : 0.005 0.079 6157 Dihedral : 16.274 177.491 13464 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.95 % Rotamer: Outliers : 1.10 % Allowed : 13.07 % Favored : 85.83 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4539 helix: 1.21 (0.11), residues: 2282 sheet: 0.65 (0.22), residues: 587 loop : -1.37 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 228 TYR 0.016 0.001 TYR I 351 PHE 0.029 0.002 PHE G 8 TRP 0.012 0.001 TRP H 435 HIS 0.007 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00573 (35605) covalent geometry : angle 0.70575 (48094) hydrogen bonds : bond 0.15656 ( 1988) hydrogen bonds : angle 5.70665 ( 5787) Misc. bond : bond 0.53253 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.7870 (t0) cc_final: 0.7458 (t0) REVERT: D 24 ARG cc_start: 0.7546 (ttt180) cc_final: 0.7293 (mtp180) REVERT: E 170 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7162 (mtpp) outliers start: 42 outliers final: 24 residues processed: 270 average time/residue: 0.7667 time to fit residues: 245.4883 Evaluate side-chains 252 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 342 ASP Chi-restraints excluded: chain I residue 391 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS D 515 GLN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 514 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.087128 restraints weight = 55863.510| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.40 r_work: 0.3036 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35606 Z= 0.130 Angle : 0.573 8.440 48094 Z= 0.292 Chirality : 0.043 0.165 5698 Planarity : 0.004 0.066 6157 Dihedral : 9.234 179.171 4979 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 1.94 % Allowed : 12.28 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.13), residues: 4539 helix: 1.90 (0.11), residues: 2294 sheet: 0.66 (0.22), residues: 579 loop : -1.28 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 397 TYR 0.012 0.001 TYR F 282 PHE 0.021 0.001 PHE A 367 TRP 0.008 0.001 TRP A 21 HIS 0.006 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00280 (35605) covalent geometry : angle 0.57282 (48094) hydrogen bonds : bond 0.05359 ( 1988) hydrogen bonds : angle 4.04471 ( 5787) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 247 time to evaluate : 1.395 Fit side-chains REVERT: B 133 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: B 196 HIS cc_start: 0.7636 (OUTLIER) cc_final: 0.7285 (m-70) REVERT: B 230 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7735 (t0) REVERT: B 315 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7828 (pp) REVERT: D 158 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8085 (t70) REVERT: D 360 GLN cc_start: 0.8406 (tt0) cc_final: 0.8175 (tt0) REVERT: E 17 ASP cc_start: 0.7090 (t0) cc_final: 0.6880 (t0) REVERT: E 170 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8036 (mmtm) REVERT: E 247 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7840 (p0) REVERT: E 353 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8288 (tpt) REVERT: E 416 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8162 (mt) REVERT: H 20 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7462 (mmm160) REVERT: H 270 MET cc_start: 0.8346 (mtm) cc_final: 0.8145 (mtp) outliers start: 74 outliers final: 24 residues processed: 296 average time/residue: 0.7586 time to fit residues: 268.9903 Evaluate side-chains 256 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 391 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 122 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 357 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 355 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 442 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 67 ASN C 252 ASN D 515 GLN F 296 ASN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 514 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.086388 restraints weight = 56195.687| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.41 r_work: 0.3025 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35606 Z= 0.135 Angle : 0.556 8.188 48094 Z= 0.280 Chirality : 0.042 0.168 5698 Planarity : 0.004 0.062 6157 Dihedral : 8.886 175.250 4958 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.66 % Favored : 96.32 % Rotamer: Outliers : 2.26 % Allowed : 13.04 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.13), residues: 4539 helix: 2.11 (0.11), residues: 2294 sheet: 0.67 (0.22), residues: 595 loop : -1.25 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 480 TYR 0.012 0.001 TYR F 282 PHE 0.026 0.001 PHE G 8 TRP 0.009 0.001 TRP H 435 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00312 (35605) covalent geometry : angle 0.55575 (48094) hydrogen bonds : bond 0.05180 ( 1988) hydrogen bonds : angle 3.82009 ( 5787) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 241 time to evaluate : 1.398 Fit side-chains REVERT: A 111 GLU cc_start: 0.8428 (pt0) cc_final: 0.8135 (tt0) REVERT: B 133 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: B 196 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.7237 (m-70) REVERT: B 230 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7843 (t0) REVERT: B 315 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7876 (pp) REVERT: C 413 GLU cc_start: 0.8141 (mp0) cc_final: 0.7849 (mp0) REVERT: D 96 LYS cc_start: 0.8290 (tppt) cc_final: 0.8043 (tppt) REVERT: D 158 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8079 (t70) REVERT: E 204 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8249 (mtpp) REVERT: E 353 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8281 (tpt) REVERT: E 416 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8197 (mt) REVERT: F 402 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7883 (tm-30) REVERT: F 447 GLU cc_start: 0.6893 (mp0) cc_final: 0.6393 (mm-30) REVERT: H 20 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7488 (mmm160) REVERT: H 270 MET cc_start: 0.8399 (mtm) cc_final: 0.8153 (mtp) REVERT: I 157 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8565 (mtt180) REVERT: I 415 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7836 (mp0) outliers start: 86 outliers final: 41 residues processed: 297 average time/residue: 0.7742 time to fit residues: 274.8609 Evaluate side-chains 274 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 157 ARG Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 482 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 324 optimal weight: 7.9990 chunk 76 optimal weight: 0.0670 chunk 203 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 438 optimal weight: 0.8980 chunk 327 optimal weight: 9.9990 chunk 345 optimal weight: 0.9980 chunk 342 optimal weight: 0.0070 chunk 154 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 67 ASN C 30 GLN D 515 GLN E 10 ASN E 73 ASN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.090047 restraints weight = 55612.114| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.41 r_work: 0.3070 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35606 Z= 0.098 Angle : 0.513 8.012 48094 Z= 0.256 Chirality : 0.041 0.159 5698 Planarity : 0.003 0.061 6157 Dihedral : 8.085 162.389 4953 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 1.81 % Allowed : 14.33 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.13), residues: 4539 helix: 2.35 (0.11), residues: 2301 sheet: 0.68 (0.22), residues: 586 loop : -1.10 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.013 0.001 TYR H 232 PHE 0.027 0.001 PHE G 8 TRP 0.008 0.001 TRP H 435 HIS 0.003 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00203 (35605) covalent geometry : angle 0.51327 (48094) hydrogen bonds : bond 0.03791 ( 1988) hydrogen bonds : angle 3.55691 ( 5787) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 1.313 Fit side-chains REVERT: A 1 MET cc_start: 0.6367 (ptp) cc_final: 0.5616 (ppp) REVERT: A 6 HIS cc_start: 0.8360 (t70) cc_final: 0.8113 (t-90) REVERT: A 73 MET cc_start: 0.8390 (mpp) cc_final: 0.8070 (mpm) REVERT: A 111 GLU cc_start: 0.8391 (pt0) cc_final: 0.8090 (tt0) REVERT: B 133 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: B 196 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6972 (m-70) REVERT: B 230 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7779 (t0) REVERT: B 249 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8103 (ppp) REVERT: C 413 GLU cc_start: 0.8116 (mp0) cc_final: 0.7865 (mp0) REVERT: D 96 LYS cc_start: 0.7969 (tppt) cc_final: 0.7734 (tppt) REVERT: D 158 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8001 (t70) REVERT: D 360 GLN cc_start: 0.8369 (tt0) cc_final: 0.8116 (tt0) REVERT: E 204 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8057 (mtpp) REVERT: E 416 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8020 (mt) REVERT: F 128 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8604 (mm) REVERT: F 402 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7752 (tm-30) REVERT: F 446 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.5622 (mmm) REVERT: F 447 GLU cc_start: 0.6930 (mp0) cc_final: 0.6362 (mm-30) REVERT: H 20 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7403 (mmm160) REVERT: H 270 MET cc_start: 0.8177 (mtm) cc_final: 0.7933 (mtp) REVERT: I 333 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8282 (pp) REVERT: I 338 ASP cc_start: 0.7879 (p0) cc_final: 0.7584 (p0) REVERT: I 415 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7776 (mp0) outliers start: 69 outliers final: 23 residues processed: 312 average time/residue: 0.7445 time to fit residues: 278.2080 Evaluate side-chains 266 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 415 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 191 optimal weight: 0.9980 chunk 331 optimal weight: 0.0980 chunk 182 optimal weight: 8.9990 chunk 379 optimal weight: 4.9990 chunk 389 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 198 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 373 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS C 252 ASN D 515 GLN I 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088631 restraints weight = 56062.336| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.41 r_work: 0.3043 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35606 Z= 0.109 Angle : 0.520 7.906 48094 Z= 0.259 Chirality : 0.041 0.159 5698 Planarity : 0.003 0.063 6157 Dihedral : 7.870 158.815 4951 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 1.92 % Allowed : 14.96 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.13), residues: 4539 helix: 2.41 (0.11), residues: 2299 sheet: 0.72 (0.22), residues: 596 loop : -1.06 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 516 TYR 0.013 0.001 TYR H 232 PHE 0.027 0.001 PHE G 8 TRP 0.009 0.001 TRP H 435 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00244 (35605) covalent geometry : angle 0.52049 (48094) hydrogen bonds : bond 0.04143 ( 1988) hydrogen bonds : angle 3.53068 ( 5787) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 239 time to evaluate : 1.374 Fit side-chains REVERT: A 6 HIS cc_start: 0.8331 (t70) cc_final: 0.8089 (t-90) REVERT: A 73 MET cc_start: 0.8401 (mpp) cc_final: 0.8114 (mpm) REVERT: B 67 ASN cc_start: 0.7638 (t160) cc_final: 0.7271 (t0) REVERT: B 133 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6529 (mp0) REVERT: B 230 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7836 (t0) REVERT: B 235 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8147 (mmmt) REVERT: B 315 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7757 (pp) REVERT: B 372 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.7965 (pt) REVERT: C 413 GLU cc_start: 0.8130 (mp0) cc_final: 0.7863 (mp0) REVERT: D 93 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7908 (mp0) REVERT: D 96 LYS cc_start: 0.8025 (tppt) cc_final: 0.7730 (tppt) REVERT: D 158 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8033 (t70) REVERT: D 360 GLN cc_start: 0.8387 (tt0) cc_final: 0.8126 (tt0) REVERT: E 204 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8195 (mtpp) REVERT: E 416 LEU cc_start: 0.8345 (tp) cc_final: 0.8006 (mt) REVERT: F 446 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6115 (mmm) REVERT: H 20 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7555 (mmm160) REVERT: H 270 MET cc_start: 0.8204 (mtm) cc_final: 0.7925 (mtp) REVERT: I 157 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8323 (mmt180) REVERT: I 261 LYS cc_start: 0.7957 (mppt) cc_final: 0.7750 (mptt) REVERT: I 333 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8280 (pp) REVERT: I 338 ASP cc_start: 0.7838 (p0) cc_final: 0.7635 (p0) REVERT: I 415 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: I 520 GLU cc_start: 0.8110 (pt0) cc_final: 0.7813 (pt0) outliers start: 73 outliers final: 30 residues processed: 292 average time/residue: 0.7357 time to fit residues: 257.8174 Evaluate side-chains 268 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 430 MET Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 157 ARG Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 415 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 204 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 250 optimal weight: 0.4980 chunk 255 optimal weight: 2.9990 chunk 343 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 324 optimal weight: 2.9990 chunk 349 optimal weight: 0.9990 chunk 313 optimal weight: 0.0470 overall best weight: 1.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 67 ASN C 252 ASN D 515 GLN I 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.088168 restraints weight = 56212.346| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.42 r_work: 0.3057 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35606 Z= 0.110 Angle : 0.523 8.973 48094 Z= 0.259 Chirality : 0.041 0.154 5698 Planarity : 0.003 0.064 6157 Dihedral : 7.659 155.654 4951 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 1.99 % Allowed : 14.91 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.13), residues: 4539 helix: 2.47 (0.11), residues: 2298 sheet: 0.72 (0.22), residues: 596 loop : -1.04 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 516 TYR 0.013 0.001 TYR H 232 PHE 0.011 0.001 PHE D 364 TRP 0.010 0.001 TRP H 435 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00247 (35605) covalent geometry : angle 0.52258 (48094) hydrogen bonds : bond 0.04222 ( 1988) hydrogen bonds : angle 3.50730 ( 5787) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 237 time to evaluate : 1.314 Fit side-chains REVERT: A 73 MET cc_start: 0.8558 (mpp) cc_final: 0.8264 (mpm) REVERT: B 67 ASN cc_start: 0.7872 (t0) cc_final: 0.7557 (t160) REVERT: B 133 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: B 157 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7297 (mp) REVERT: B 196 HIS cc_start: 0.7218 (OUTLIER) cc_final: 0.6932 (m-70) REVERT: B 235 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8211 (mmmt) REVERT: B 249 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8047 (ppp) REVERT: B 315 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7867 (pp) REVERT: B 372 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8014 (pt) REVERT: D 93 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7931 (mp0) REVERT: D 96 LYS cc_start: 0.8210 (tppt) cc_final: 0.7933 (tppt) REVERT: D 158 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8149 (t70) REVERT: D 360 GLN cc_start: 0.8455 (tt0) cc_final: 0.8216 (tt0) REVERT: E 204 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8286 (mtpp) REVERT: E 353 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8220 (tpt) REVERT: E 416 LEU cc_start: 0.8470 (tp) cc_final: 0.8141 (mt) REVERT: H 270 MET cc_start: 0.8306 (mtm) cc_final: 0.8036 (mtp) REVERT: I 157 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8375 (mmt180) REVERT: I 261 LYS cc_start: 0.8143 (mppt) cc_final: 0.7942 (mppt) REVERT: I 333 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8360 (pp) REVERT: I 415 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: I 520 GLU cc_start: 0.8150 (pt0) cc_final: 0.7869 (pt0) outliers start: 76 outliers final: 37 residues processed: 291 average time/residue: 0.7358 time to fit residues: 256.4632 Evaluate side-chains 277 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 506 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain G residue 430 MET Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 157 ARG Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 514 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 415 optimal weight: 8.9990 chunk 436 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 331 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 387 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 375 GLN D 515 GLN I 84 GLN I 514 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.083640 restraints weight = 56354.963| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.42 r_work: 0.2965 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35606 Z= 0.183 Angle : 0.596 8.264 48094 Z= 0.299 Chirality : 0.044 0.168 5698 Planarity : 0.004 0.067 6157 Dihedral : 7.930 162.387 4947 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.92 % Rotamer: Outliers : 2.23 % Allowed : 15.04 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.13), residues: 4539 helix: 2.26 (0.11), residues: 2296 sheet: 0.65 (0.22), residues: 593 loop : -1.14 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 516 TYR 0.015 0.001 TYR H 232 PHE 0.021 0.002 PHE G 8 TRP 0.012 0.001 TRP H 435 HIS 0.005 0.001 HIS I 65 Details of bonding type rmsd covalent geometry : bond 0.00448 (35605) covalent geometry : angle 0.59595 (48094) hydrogen bonds : bond 0.05944 ( 1988) hydrogen bonds : angle 3.74717 ( 5787) Misc. bond : bond 0.00121 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 235 time to evaluate : 1.415 Fit side-chains REVERT: A 111 GLU cc_start: 0.8231 (pt0) cc_final: 0.7465 (pm20) REVERT: B 26 GLU cc_start: 0.8222 (pm20) cc_final: 0.7980 (pm20) REVERT: B 67 ASN cc_start: 0.7855 (t0) cc_final: 0.7527 (t160) REVERT: B 68 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7921 (t70) REVERT: B 133 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: B 157 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7257 (mp) REVERT: B 196 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.7051 (m-70) REVERT: B 285 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7812 (t0) REVERT: B 315 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7987 (pp) REVERT: C 185 MET cc_start: 0.7681 (mtm) cc_final: 0.7140 (ptp) REVERT: D 96 LYS cc_start: 0.8238 (tppt) cc_final: 0.7913 (tppt) REVERT: D 158 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8216 (t70) REVERT: E 204 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8339 (mtpp) REVERT: E 353 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8197 (tpt) REVERT: E 416 LEU cc_start: 0.8503 (tp) cc_final: 0.8136 (mt) REVERT: F 128 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8406 (mm) REVERT: G 182 THR cc_start: 0.7576 (OUTLIER) cc_final: 0.7029 (p) REVERT: H 197 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6959 (ptmt) REVERT: H 270 MET cc_start: 0.8330 (mtm) cc_final: 0.8034 (mtp) REVERT: I 157 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8516 (mtt180) REVERT: I 415 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: I 520 GLU cc_start: 0.8187 (pt0) cc_final: 0.7866 (pt0) outliers start: 85 outliers final: 42 residues processed: 301 average time/residue: 0.6788 time to fit residues: 246.1644 Evaluate side-chains 283 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 227 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 157 ARG Chi-restraints excluded: chain I residue 415 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 366 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 123 optimal weight: 0.0970 chunk 135 optimal weight: 7.9990 chunk 427 optimal weight: 3.9990 chunk 423 optimal weight: 4.9990 chunk 442 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 514 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.099235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.082433 restraints weight = 56525.671| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.42 r_work: 0.2945 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 35606 Z= 0.201 Angle : 0.619 10.389 48094 Z= 0.313 Chirality : 0.045 0.177 5698 Planarity : 0.004 0.070 6157 Dihedral : 8.021 165.115 4947 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.03 % Rotamer: Outliers : 2.10 % Allowed : 15.62 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.13), residues: 4539 helix: 2.12 (0.11), residues: 2284 sheet: 0.53 (0.22), residues: 595 loop : -1.23 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 162 TYR 0.015 0.001 TYR H 232 PHE 0.016 0.002 PHE E 362 TRP 0.012 0.001 TRP C 484 HIS 0.006 0.001 HIS G 201 Details of bonding type rmsd covalent geometry : bond 0.00498 (35605) covalent geometry : angle 0.61884 (48094) hydrogen bonds : bond 0.06269 ( 1988) hydrogen bonds : angle 3.84157 ( 5787) Misc. bond : bond 0.00132 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 228 time to evaluate : 1.349 Fit side-chains REVERT: A 19 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8034 (tmtt) REVERT: A 111 GLU cc_start: 0.8193 (pt0) cc_final: 0.7416 (pm20) REVERT: A 205 GLU cc_start: 0.3644 (mm-30) cc_final: 0.3403 (mt-10) REVERT: A 436 PHE cc_start: 0.1357 (OUTLIER) cc_final: 0.1141 (t80) REVERT: B 26 GLU cc_start: 0.8249 (pm20) cc_final: 0.7991 (pm20) REVERT: B 67 ASN cc_start: 0.7934 (t0) cc_final: 0.7707 (t160) REVERT: B 133 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: B 157 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7163 (mp) REVERT: B 196 HIS cc_start: 0.7408 (OUTLIER) cc_final: 0.7207 (m-70) REVERT: B 266 MET cc_start: 0.8721 (mmm) cc_final: 0.8414 (mmm) REVERT: B 285 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7732 (t0) REVERT: B 315 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8092 (pp) REVERT: C 185 MET cc_start: 0.7602 (mtm) cc_final: 0.6959 (ptp) REVERT: D 96 LYS cc_start: 0.8216 (tppt) cc_final: 0.7859 (tppt) REVERT: D 158 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8145 (t70) REVERT: E 204 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8344 (mtpp) REVERT: E 284 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8277 (ttpt) REVERT: E 353 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8253 (tpt) REVERT: F 128 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8442 (mm) REVERT: G 182 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7000 (p) REVERT: G 500 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8331 (tt0) REVERT: H 197 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7049 (ptmt) REVERT: H 270 MET cc_start: 0.8292 (mtm) cc_final: 0.8017 (mtp) REVERT: I 157 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8494 (mtt180) REVERT: I 339 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8633 (mp) REVERT: I 415 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: I 520 GLU cc_start: 0.8283 (pt0) cc_final: 0.7963 (pt0) outliers start: 80 outliers final: 43 residues processed: 286 average time/residue: 0.7208 time to fit residues: 245.3559 Evaluate side-chains 284 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 225 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 157 ARG Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 415 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 107 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 252 optimal weight: 0.9980 chunk 356 optimal weight: 0.5980 chunk 353 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 333 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 388 optimal weight: 0.9990 chunk 357 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.104049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087361 restraints weight = 55953.787| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.39 r_work: 0.3045 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 35606 Z= 0.108 Angle : 0.537 8.697 48094 Z= 0.269 Chirality : 0.041 0.171 5698 Planarity : 0.003 0.063 6157 Dihedral : 7.252 152.626 4946 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.63 % Allowed : 16.04 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.13), residues: 4539 helix: 2.40 (0.11), residues: 2294 sheet: 0.62 (0.22), residues: 586 loop : -1.11 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 162 TYR 0.015 0.001 TYR H 232 PHE 0.027 0.001 PHE G 8 TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00231 (35605) covalent geometry : angle 0.53675 (48094) hydrogen bonds : bond 0.04216 ( 1988) hydrogen bonds : angle 3.58098 ( 5787) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 244 time to evaluate : 1.393 Fit side-chains REVERT: A 19 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8087 (tmtt) REVERT: A 111 GLU cc_start: 0.8282 (pt0) cc_final: 0.7511 (pm20) REVERT: A 205 GLU cc_start: 0.3694 (mm-30) cc_final: 0.3491 (mt-10) REVERT: A 220 PRO cc_start: 0.6203 (Cg_endo) cc_final: 0.5707 (Cg_exo) REVERT: B 26 GLU cc_start: 0.8221 (pm20) cc_final: 0.8003 (pm20) REVERT: B 67 ASN cc_start: 0.7864 (t0) cc_final: 0.7604 (t160) REVERT: B 133 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: B 315 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8050 (pp) REVERT: B 443 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: C 185 MET cc_start: 0.7517 (mtm) cc_final: 0.6987 (ptp) REVERT: D 96 LYS cc_start: 0.8289 (tppt) cc_final: 0.7996 (tppt) REVERT: E 204 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8242 (mtpp) REVERT: E 416 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8221 (mt) REVERT: F 447 GLU cc_start: 0.7459 (mp0) cc_final: 0.6801 (mm-30) REVERT: G 500 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8380 (tt0) REVERT: H 270 MET cc_start: 0.8286 (mtm) cc_final: 0.8033 (mtp) REVERT: H 367 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7679 (mmpt) REVERT: H 521 ASP cc_start: 0.8383 (p0) cc_final: 0.8161 (p0) REVERT: I 157 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8326 (mmt180) REVERT: I 415 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: I 520 GLU cc_start: 0.8196 (pt0) cc_final: 0.7932 (pt0) outliers start: 62 outliers final: 35 residues processed: 286 average time/residue: 0.7348 time to fit residues: 251.9401 Evaluate side-chains 274 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 157 ARG Chi-restraints excluded: chain I residue 415 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 290 optimal weight: 0.0170 chunk 187 optimal weight: 0.7980 chunk 432 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 449 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 362 optimal weight: 4.9990 chunk 279 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 392 optimal weight: 0.8980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.088871 restraints weight = 55810.790| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.40 r_work: 0.3072 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 35606 Z= 0.102 Angle : 0.530 9.197 48094 Z= 0.264 Chirality : 0.041 0.152 5698 Planarity : 0.003 0.066 6157 Dihedral : 6.969 153.959 4946 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.26 % Allowed : 16.82 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.13), residues: 4539 helix: 2.52 (0.11), residues: 2301 sheet: 0.68 (0.22), residues: 581 loop : -1.01 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 403 TYR 0.016 0.001 TYR H 232 PHE 0.011 0.001 PHE A 436 TRP 0.011 0.001 TRP H 435 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00220 (35605) covalent geometry : angle 0.52952 (48094) hydrogen bonds : bond 0.03804 ( 1988) hydrogen bonds : angle 3.45806 ( 5787) Misc. bond : bond 0.00010 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 247 time to evaluate : 1.439 Fit side-chains REVERT: A 1 MET cc_start: 0.6310 (ptp) cc_final: 0.5684 (ppp) REVERT: A 19 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8055 (tmtt) REVERT: A 111 GLU cc_start: 0.8347 (pt0) cc_final: 0.7605 (pm20) REVERT: B 67 ASN cc_start: 0.7859 (t0) cc_final: 0.7653 (t160) REVERT: B 133 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: B 235 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8237 (mmmt) REVERT: B 315 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8028 (pp) REVERT: B 443 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: C 185 MET cc_start: 0.7443 (mtm) cc_final: 0.6938 (ptp) REVERT: D 96 LYS cc_start: 0.8261 (tppt) cc_final: 0.7995 (tppt) REVERT: D 360 GLN cc_start: 0.8488 (tt0) cc_final: 0.8231 (tt0) REVERT: E 416 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8220 (mt) REVERT: F 447 GLU cc_start: 0.7489 (mp0) cc_final: 0.6841 (mm-30) REVERT: G 500 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8458 (tt0) REVERT: H 270 MET cc_start: 0.8340 (mtm) cc_final: 0.8103 (mtp) REVERT: H 521 ASP cc_start: 0.8402 (p0) cc_final: 0.8181 (p0) REVERT: I 415 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7817 (mp0) outliers start: 48 outliers final: 32 residues processed: 282 average time/residue: 0.7114 time to fit residues: 241.0232 Evaluate side-chains 276 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 238 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 455 CYS Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 157 ARG Chi-restraints excluded: chain I residue 415 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 174 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 301 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 514 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.084536 restraints weight = 56352.143| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.40 r_work: 0.3003 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35606 Z= 0.169 Angle : 0.593 12.181 48094 Z= 0.296 Chirality : 0.043 0.161 5698 Planarity : 0.004 0.068 6157 Dihedral : 7.239 159.234 4946 Min Nonbonded Distance : 1.567 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.34 % Allowed : 17.03 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.13), residues: 4539 helix: 2.35 (0.11), residues: 2289 sheet: 0.65 (0.22), residues: 582 loop : -1.10 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 516 TYR 0.017 0.001 TYR H 232 PHE 0.026 0.002 PHE G 8 TRP 0.011 0.001 TRP H 435 HIS 0.005 0.001 HIS I 65 Details of bonding type rmsd covalent geometry : bond 0.00414 (35605) covalent geometry : angle 0.59269 (48094) hydrogen bonds : bond 0.05442 ( 1988) hydrogen bonds : angle 3.65030 ( 5787) Misc. bond : bond 0.00071 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10093.50 seconds wall clock time: 172 minutes 57.77 seconds (10377.77 seconds total)